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Interpretive Summary: The Colorado potato beetle (CPB), Leptinotarsa decemlineata (Say), is the major defoliator of potato and also feeds on tomato and eggplant. The center of origin of L. decemlineata is believed to be southern Mexico and the beetle experienced a rapid range expansion in the mid-1800s. L. decemlineata was first reported as a pest of potato, tomato and eggplant in 1859-62 in the Iowa, Kansas, and Nebraska region of the central plains of North America; by 1877 it was discovered in potato fields in Germany, and it was established in Europe by 1921. The Colorado potato beetle is now endemic in most of the potato growing regions worldwide. The plasticity of the CPB’s diapause response played a key role in its range expansion. Growing evidence indicated that mobile genomic elements known as transposable elements (TEs) that can comprise 2% to 90% of most eukaryotic genomes are key players in determining the plasticity of an organism’s physiological traits. We report here the isolation of four families of novel TEs known as miniature subterminal inverted repeat transposable elements (MSITEs) from the Colorado potato beetle. Three families of these new MSITEs are inserted in the introns of two diapause-regulated genes and within the promoter region of two other diapause-regulated genes. During the preparatory phase of diapause, transcripts with homology to one family of MSITEs are expressed. The presence of MSITEs in the promoters, introns and mature transcripts of diapause-regulated genes raises the question of the role of these TEs in the evolution and regulation of diapause.

Technical Abstract: Determining the genomic structure of diapause-associated transcripts (DAT) -2 and -3 led to the isolation of four novel miniature subterminal inverted repeat-like elements (MSITE): Mild-1, -2, -3 and -4. Mild-1a is inserted within the first intron of diapause protein-1. Mild-1a is 284 bp in length, has a 14 bp target site duplication and three sets of subterminal inverted repeats. The second element, Mild-2a, is inserted within the 3' terminus of Mild-1a. Mild-2a is 29 bp long with a 3 bp target site duplication and one set of subterminal inverted repeats. Using primers based on Mild-1, genomic clones were developed leading to the isolation of Mild-3a. Mild-3a shares 60% identity with Mild-1a, is 253 bp long, has a 9 bp target site duplication and has one set of subterminal inverted repeats. Mild-4a is inserted within the first intron of DAT-2 and is 227 bp in length with a 12 bp target site duplication. Mild-4a appears to be an intermediate form between a miniature inverted repeat transposable element (MITE) and a MSITE because the 5' inverted repeat is terminal (i.e., adjacent to the target site duplication) as in MITEs, but the 3' inverted repeat is separated (in this case, by 33 bp) from the 3' target site duplication as in MSITEs. The target site duplications of Mild-1, -3 and -4 families share a common conserved core of AATTT. All of the transposable elements are AT rich and are able to form hairpin structures. Within the promoter region of DAT-3 is a 163 bp sequence (Mild-1b) that shares 77% identity to the 3' terminus of Mild-1a. Mild-4a has identity to 25 and 53 bp regions within the promoter of the juvenile hormone esterase B gene. Southern blot analysis revealed the presence of Mild-1 and -3 elements in both Leptinotarsa decemlineata and Leptinotarsa juncta indicating that these elements are ancestral to the L. decemlineata, L. juncta separation.